Registry alteration in Dynein's microtubule-binding domain: A AAA domain-guided event

Abstract

Dynein, a motor protein, harnesses chemical energy from ATP hydrolysis to generate mechanical output as it travels along microtubular tracks. Essential to this process is the microtubule-binding domain (MTBD), which facilitates the interaction with and detachment from microtubules. Previous studies have proposed that the mechanism governing this interaction is primarily driven by the coiled-coil stalk attached to the MTBD. However, conflicting arguments suggest the presence of two-way communications, where the binding and unbinding mechanisms may also influence the nucleotide state of dynein. In this study, we employed all-atom explicit solvent simulations, enhanced sampling techniques, and coarse-grained methodologies to systematically investigate the effects of stalk and MT on the structural stabilities of different conformations of MTBD and their sequence of events during the transition from one to another. We found that the globular MTBD domain without stalk and MT predominantly resides in its weak binding configuration. Upon introduction of a limited length of stalk and interaction with MT, a balance between the strong and weak binding configurations is restored. Further introduction of the full-length stalk and interaction with MT strengthen the kinetic stability of these two configurations. We have also explored the sequence of events of the relevant transition between these two states using coarse-grained simulation protocols both in the presence and absence of interaction with MT. In the absence of MT interactions, we found a mixed conformational state of the system that corresponds to the already published crystal structure of Dynein. In the presence of MT, the conformational change of the stalk precedes the conformational change of the MTBD globular domain. Our findings support the view that the nucleotide state of the AAA+ ring determines the state of the MTBD domain through stalk, shedding light on the intricate mechanisms governing dynein's interaction with microtubules.